Hi Rashimi, no idea what is causing this, as you say the scripts look OK. Have you tried re-running the longitudinal run from scratch, to make sure this is not caused by earlier data or by some I/O problem?
Best, Martin On Fri, 2012-05-25 at 16:41 +0000, Rashmi Singh wrote: > Thanks Martin, > I deleted the older runs for base run and started a new run with -use– > mritotal flag in the command line: > Following is my script for base run for the subjects ( AA543 and > AA550) that were giving me errors other than AA510.T1 > > > #!/bin/bash > > > SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer > export SUBJECTS_DIR > > > recon-all -base AA543.long1 -tp AA543.T0 -tp AA543.T2 -tp AA543.T3 > -use-mritotal -all </dev/null&> FSAA543.long1 & > recon-all -base AA550.long1 -tp AA550.T1 -tp AA550.T2 -tp AA550.T3 > -use-mritotal -all </dev/null&> FSAA550.long1 & > > > The base runs for AA453, AA550 and AA510 completed without error, > So I ran the long run for each time point. > My script for that was > > > #!/bin/bash > > > SUBJECTS_DIR=~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer > export SUBJECTS_DIR > > > recon-all -long AA543.T0 AA543.long1 -use-mritotal -all </dev/null&> > FSAA543.T0long & > recon-all -long AA543.T2 AA543.long1 -use-mritotal -all </dev/null&> > FSAA543.T2long & > recon-all -long AA543.T3 AA543.long1 -use-mritotal -all </dev/null&> > FSAA543.T3long & > recon-all -long AA550.T1 AA550.long1 -use-mritotal -all </dev/null&> > FSAA550.T1long & > recon-all -long AA550.T2 AA550.long1 -use-mritotal -all </dev/null&> > FSAA550.T2long & > recon-all -long AA550.T3 AA550.long1 -use-mritotal -all </dev/null&> > FSAA550.T3long & > recon-all -long AA510.T1 AA510.long1 -use-mritotal -all </dev/null&> > FSAA550.T1long & > recon-all -long AA510.T2 AA510.long1 -use-mritotal -all </dev/null&> > FSAA550.T2long & > recon-all -long AA510.T7 AA510.long1 -use-mritotal -all </dev/null&> > FSAA550.T1long & > > > > > The long run for All AA510 time points and AA543.T2 and AA550.T1 > and .T3 were completed without error, however surprisingly AA550.T2, > AA543.T1 and AA543.T3 exited with error, the srcipt log didn't define > any error other than suggesting the error to be reported. > All incomplete runs exited at the same point. Attached are the script > log of the runs that exited with error. I am also atatching the log > file for AA543.T2 which completed the long run > > > > > > > > > > > Message: 7 > Date: Thu, 24 May 2012 18:42:17 -0400 > From: Martin Reuter <[email protected]> > Subject: Re: [Freesurfer] error longitudinal processing > To: Rashmi Singh <[email protected]> > Cc: "[email protected]" <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=utf-8 > > > Hi Rashmi, > > > the command line for running the base (subject-template) should be: > recon-all -base AA510 -tp AA510.T1 -tp AA510.T2 -tp AA510.T7 -all > we usually don't put the '.long' after the base. > > > I don't think this is causing your problem however. In your case for > some reason the talairach transform fails. It could be that something > earlier fails. > > > You should > > > - check the .....AA510.long/mri/norm_template.mgz if it looks OK (it > is > the average of your time points). > also the .....AA510.long/mri/orig.mgz should look good. > > > if they are OK, you need to find out why the talairach reg is failing > .....AA510.long/mri/transforms/talairach.xfm > > > forgot the command for it, but it is the same as in cross sectional > processing. > > > What is weird is your log says this: > "INFO: transforms/talairach.xfm already exists! > The new transforms/talairach.auto.xfm will not be copied to > transforms/talairach.xfm > This is done to retain any edits made to transforms/talairach.xfm" > > > So probably you have an old talairach.xfm there. > I think deleting the AA510.long and rerunning the base from scratch > may > fix everything. So maybe you want to try that first. > > > Best, Martin > > > On Tue, 2012-05-22 at 15:00 +0000, Rashmi Singh wrote: > Hello, > I ran longitudinal processing which exited with errors. I am > attaching the output file. > Please advise why this error occurred. The recon ?all run ran > perfectly for all the time points for this subject. > My command was as follows: > recon-all -base AA510.long -tp AA510.T1 -tp AA510.T2 -tp > AA510.T7 -all > </dev/null&> FSAA510.long & > > > My all other subjects longitudinal run completed without > error. > Thanks, > Rashmi > > > ______________________________________________________________________ > > This document may contain information covered under the Privacy Act, 5 > USC 552(a), and/or the Health Insurance Portability and Accountability > Act (PL 104-191) and its various implementing regulations and must be > protected in accordance with those provisions. Healthcare information > is personal and sensitive and must be treated accordingly. 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